Question

I am trying to write a python code to match things from two lists in python.

One tab-delimited file looks like this:

COPB2

KLMND7

BLCA8

while the other file2 has a long list of similar looking “names”, if you will. There should be some identical matches in the file, which I have succeeded in identifying and writing out to a new file. The problem is when there are additional characters at the end of one of the “names”. For example, COPB2 from above should match COPB2A in file2, but it does not. Similarly KLMND7 should match KLMND79. Should I use regular expressions? Make them into strings? Any ideas are helpful, thank you!

What I have worked on so far, after the first response seen below:

with open(in_file1, "r") as names:
for line in names:
    file1_list = [i.strip() for i in line.split()]
    file1_str = str(file1_list)

with open(in_file2, "r") as symbols:
for line in symbols:
    items = line.split("\t")
    items = str(items)
    matches = items.startswith(file1_str)
    print matches

This code returns False when I know there should be some matches.

Answer 1

string.startswith() No need for regex, if it’s only trailing characters

>>> g = "COPB2A"
>>> f = "COPB2"
>>> g.startswith(f)
True

Here is a working piece of code:

file1_list = []
with open(in_file1, "r") as names:
    for line in names:
        line_items = line.split()
        for item in line_items:
            file1_list.append(item)

matches = []
with open(in_file2, "r") as symbols:
    for line in symbols:
        file2_items = line.split()
        for file2_item in file2_items:
            for file1_item in file1_list:
                if file2_item.startswith(file1_item):
                    matches.append(file2_item)
                    print file2_item
print matches

It may be quite slow for large files. If it’s unacceptable, I could try to think about how to optimize it.